DESCRIPTION

This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used to the SeqIO system it, we are deliberately using the same pattern).

Once you get a SearchIO object, calling next_result() gives you back a Bio::Search::Result::ResultI compliant object, which is an object that represents one Blast/Fasta/HMMER whatever report.

Also see the SearchIO HOWTO: http://bioperl.org/howtos/SearchIO_HOWTO.html

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich & Steve Chervitz

Email jason-at-bioperl.org Email sac-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title : new
Usage : my $obj = Bio::SearchIO->new();
Function: Builds a new Bio::SearchIO object
Returns : Bio::SearchIO initialized with the correct format
Args : -file => $filename
-format => format
-fh => filehandle to attach to
-result_factory => object implementing Bio::Factory::ObjectFactoryI
-hit_factory => object implementing Bio::Factory::ObjectFactoryI
-hsp_factory => object implementing Bio::Factory::ObjectFactoryI
-writer => object implementing Bio::SearchIO::SearchWriterI
-output_format => output format, which will dynamically load writer
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model
-signif => float or scientific notation number to be used
as a P- or Expect value cutoff
-check_all_hits => boolean. Check all hits for significance against
significance criteria. Default = false.
If false, stops processing hits after the first
non-significant hit or the first hit that fails
the hit_filter call. This speeds parsing,
taking advantage of the fact that the hits are
processed in the order they appear in the report.
-min_query_len => integer to be used as a minimum for query sequence
length. Reports with query sequences below this
length will not be processed.
default = no minimum length.
-best => boolean. Only process the best hit of each report;
default = false.

_eventHandler

next_result

Title : next_result
Usage : $result = stream->next_result
Function: Reads the next ResultI object from the stream and returns it.
Certain driver modules may encounter entries in the stream that
are either misformatted or that use syntax not yet understood
by the driver. If such an incident is recoverable, e.g., by
dismissing a feature of a feature table or some other non-mandatory
part of an entry, the driver will issue a warning. In the case
of a non-recoverable situation an exception will be thrown.
Do not assume that you can resume parsing the same stream after
catching the exception. Note that you can always turn recoverable
errors into exceptions by calling $stream->verbose(2) (see
Bio::Root::RootI POD page).
Returns : A Bio::Search::Result::ResultI object
Args : n/a

write_result

Title : write_result
Usage : $stream->write_result($result_result, @other_args)
Function: Writes data from the $result_result object into the stream.
: Delegates to the to_string() method of the associated
: WriterI object.
Returns : 1 for success and 0 for error
Args : Bio::Search:Result::ResultI object,
: plus any other arguments for the Writer
Throws : Bio::Root::Exception if a Writer has not been set.

write_report

Title : write_report
Usage : $stream->write_report(SearchIO stream, @other_args)
Function: Writes data directly from the SearchIO stream object into the
: writer. This is mainly useful if one has multiple ResultI objects
: in a SearchIO stream and you don't want to reiterate header/footer
: between each call.
Returns : 1 for success and 0 for error
Args : Bio::SearchIO stream object,
: plus any other arguments for the Writer
Throws : Bio::Root::Exception if a Writer has not been set.

result_count

Title : result_count
Usage : $num = $stream->result_count;
Function: Gets the number of Blast results that have been successfully parsed
at the point of the method call. This is not the total # of results
in the file.
Returns : integer
Args : none
Throws : none

max_significance

Usage : $obj->max_significance();
Purpose : Set/Get the P or Expect value used as significance screening cutoff.
This is the value of the -signif parameter supplied to new().
Hits with P or E-value above this are skipped.
Returns : Scientific notation number with this format: 1.0e-05.
Argument : Scientific notation number or float (when setting)
Comments : Screening of significant hits uses the data provided on the
: description line. For NCBI BLAST1 and WU-BLAST, this data
: is P-value. for NCBI BLAST2 it is an Expect value.

check_all_hits

Title : check_all_hits
Usage : print "checking all hits.\n" if $obj->check_all_hits;
Purpose : Set/Get the indicator for whether or not to process all hits.
: If false, the parser will stop processing hits after the
: the first non-significance hit or the first hit that fails
: any hit filter.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)

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